TestReferenceLangevinIntegrator.cpp

/* -------------------------------------------------------------------------- *
 *                                   OpenMM                                   *
 * -------------------------------------------------------------------------- *
 * This is part of the OpenMM molecular simulation toolkit originating from   *
 * Simbios, the NIH National Center for Physics-Based Simulation of           *
 * Biological Structures at Stanford, funded under the NIH Roadmap for        *
 * Medical Research, grant U54 GM072970. See https://simtk.org.               *
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 * Portions copyright (c) 2008 Stanford University and the Authors.           *
 * Authors: Peter Eastman                                                     *
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/**
 * This tests the reference implementation of LangevinIntegrator.
 */

#include "../../../tests/AssertionUtilities.h"
#include "OpenMMContext.h"
#include "ReferencePlatform.h"
#include "StandardMMForceField.h"
#include "System.h"
#include "LangevinIntegrator.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include "../src/sfmt/SFMT.h"
#include <iostream>
#include <vector>

using namespace OpenMM;
using namespace std;

const double TOL = 1e-5;

void testSingleBond() {
    ReferencePlatform platform;
    System system(2, 0);
    system.setAtomMass(0, 2.0);
    system.setAtomMass(1, 2.0);
    LangevinIntegrator integrator(0, 0.1, 0.01);
    StandardMMForceField* forceField = new StandardMMForceField(2, 1, 0, 0, 0, 0);
    forceField->setBondParameters(0, 0, 1, 1.5, 1);
    system.addForce(forceField);
    OpenMMContext context(system, integrator, platform);
    vector<Vec3> positions(2);
    positions[0] = Vec3(-1, 0, 0);
    positions[1] = Vec3(1, 0, 0);
    context.setPositions(positions);
    
    // This is simply a damped harmonic oscillator, so compare it to the analytical solution.
    
    double freq = std::sqrt(1-0.05*0.05);
    for (int i = 0; i < 1000; ++i) {
        State state = context.getState(State::Positions | State::Velocities);
        double time = state.getTime();
        double expectedDist = 1.5+0.5*std::exp(-0.05*time)*std::cos(freq*time);
        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
        ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
        double expectedSpeed = -0.5*std::exp(-0.05*time)*(0.05*std::cos(freq*time)+freq*std::sin(freq*time));
        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.02);
        ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.02);
        integrator.step(1);
    }
    
    // Not set the friction to a tiny value and see if it conserves energy.
    
    integrator.setFriction(5e-5);
    context.setPositions(positions);
    State state = context.getState(State::Energy);
    double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
    for (int i = 0; i < 1000; ++i) {
        state = context.getState(State::Energy);
        double energy = state.getKineticEnergy()+state.getPotentialEnergy();
        ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
        integrator.step(1);
    }
}

void testTemperature() {
    const int numAtoms = 8;
    const double temp = 100.0;
    ReferencePlatform platform;
    System system(numAtoms, 0);
    LangevinIntegrator integrator(temp, 2.0, 0.01);
    StandardMMForceField* forceField = new StandardMMForceField(numAtoms, 0, 0, 0, 0, 0);
    for (int i = 0; i < numAtoms; ++i) {
        system.setAtomMass(i, 2.0);
        forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
    }
    system.addForce(forceField);
    OpenMMContext context(system, integrator, platform);
    vector<Vec3> positions(numAtoms);
    for (int i = 0; i < numAtoms; ++i)
        positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
    context.setPositions(positions);
    
    // Let it equilibrate.
    
    integrator.step(10000);
    
    // Now run it for a while and see if the temperature is correct.
    
    double ke = 0.0;
    for (int i = 0; i < 1000; ++i) {
        State state = context.getState(State::Energy);
        ke += state.getKineticEnergy();
        integrator.step(1);
    }
    ke /= 1000;
    double expected = 0.5*numAtoms*3*BOLTZ*temp;
    ASSERT_EQUAL_TOL(expected, ke, 3*expected/std::sqrt(1000.0));
}

void testConstraints() {
    const int numAtoms = 8;
    const double temp = 100.0;
    ReferencePlatform platform;
    System system(numAtoms, numAtoms-1);
    LangevinIntegrator integrator(temp, 2.0, 0.01);
    StandardMMForceField* forceField = new StandardMMForceField(numAtoms, 0, 0, 0, 0, 0);
    for (int i = 0; i < numAtoms; ++i) {
        system.setAtomMass(i, 10.0);
        forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
    }
    for (int i = 0; i < numAtoms-1; ++i)
        system.setConstraintParameters(i, i, i+1, 1.0);
    system.addForce(forceField);
    OpenMMContext context(system, integrator, platform);
    vector<Vec3> positions(numAtoms);
    vector<Vec3> velocities(numAtoms);
    init_gen_rand(0);
    for (int i = 0; i < numAtoms; ++i) {
        positions[i] = Vec3(i/2, (i+1)/2, 0);
        velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
    }
    context.setPositions(positions);
    context.setVelocities(velocities);
    
    // Simulate it and see whether the constraints remain satisfied.
    
    for (int i = 0; i < 1000; ++i) {
        State state = context.getState(State::Positions);
        for (int j = 0; j < numAtoms-1; ++j) {
            Vec3 p1 = state.getPositions()[j];
            Vec3 p2 = state.getPositions()[j+1];
            double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
            ASSERT_EQUAL_TOL(1.0, dist, 2e-4);
        }
        integrator.step(1);
    }
}

int main() {
    try {
        testSingleBond();
        testTemperature();
        testConstraints();
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;
        return 1;
    }
    cout << "Done" << endl;
    return 0;
}